First, I could never be bothered to figure out how to make the damn game run from a folder other than the %appdata%\.minecraft as all my attempts to use the configuration UI or editing the profile files were in vain.

That was an annoyance but not a problem since I could use a NTFS junction to redirect the game folder a the place convenient to me which was obviously out of the system main drive.

That is no longer the case with the launcher since version 2+ was released, if I do a clean download to the default folder all work as expected but as soon as transfer the files to my game drive and create a junction to point %appdata%\.minecraft to the right place the launcher gets confused and try to use the %appdata% itself as the game folder as it cannot handle the junction.

NTFS reparse points should be transparent to an application, (and were for Minecraft) and I don't see why that should not be the case anymore, no need to mess with low level disk access for a game.